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Chunk #24 — Variance explained by SNPs within identified loci

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A saturated map of common genetic variants associated with human height.
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To further assess the robustness of this key result, we tested whether the 7,209 height-associated GWS loci are systematically enriched for trait heritability. We chose body-mass index (BMI) as a control trait, given its small genetic correlation with height (rg = −0.1, ref. 27) and found no significant enrichment of SNP-based heritability for BMI within height-associated GWS loci (Supplementary Fig. 19). Furthermore, we repeated our analysis using a random set of SNPs matched with the 12,111 height-associated GWS SNPs on EUR MAF and LD scores. We found that this control set of SNPs explained only around 27% of \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${h}_{{\rm{SNP}}}^{2}$$\end{document}hSNP2 for height, consistent with the proportion of SNPs within the loci defined by this random set of SNPs (Supplementary Figs. 18 and 19). Finally, we extended our stratified estimation of SNP-based heritability to all well-imputed common SNPs (that is, beyond the HM3 panel) and found, consistently across population groups, that although more genetic variance can be explained by common SNPs that are not included in the HM3 panel, all information remains concentrated